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Curr Biol. 2019 Jan 21;29(2):340-349.e7. doi: 10.1016/j.cub.2018.12.008. Epub 2019 Jan 10.

The Genomic Footprints of the Fall and Recovery of the Crested Ibis.

Author information

1
University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
2
China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
3
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
4
China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China; The Francis Crick Institute, London NW1 1AT, UK.
5
Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.
6
China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
7
University of Chinese Academy of Sciences, Beijing 100049, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
8
Museum of Natural History Vienna, 1st Zoological Department - Ornithology, Burgring 7, A-1010 Vienna, Austria.
9
Staatliches Museum für Naturkunde, Rosenstein 1, 70191 Stuttgart, Germany.
10
Bird Group, Department of Life Sciences, Natural History Museum, Akeman St, Tring, Herts HP23 6AP, UK.
11
Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain.
12
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway.
13
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China. Electronic address: guojie.zhang@bio.ku.dk.

Abstract

Human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. Genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of endangered species [1-4]. However, factors such as outbreeding depression [5, 6] and a reduction in available genetic diversity render the success of such approaches uncertain. An improved evaluation of the consequence of genetic restoration requires knowledge of temporal changes to genetic diversity before and after the advent of management programs. To provide such information, a growing number of studies have included small numbers of genomic loci extracted from historic and even ancient specimens [7, 8]. We extend this approach to its natural conclusion, by characterizing the complete genomic sequences of modern and historic population samples of the crested ibis (Nipponia nippon), an endangered bird that is perhaps the most successful example of how conservation effort has brought a species back from the brink of extinction. Though its once tiny population has today recovered to >2,000 individuals [9], this process was accompanied by almost half of ancestral loss of genetic variation and high deleterious mutation load. We furthermore show how genetic drift coupled to inbreeding following the population bottleneck has largely purged the ancient polymorphisms from the current population. In conclusion, we demonstrate the unique promise of exploiting genomic information held within museum samples for conservation and ecological research.

KEYWORDS:

ancient genomics; conservation genomics; demography; endangered species; extinction; genetic recovery; inbreeding; mutation load; ornithology; population genomics

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